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Modification of the dihedral parameters
you@eulerX ~$ wget http://www.cp2k.org/_media/exercises:2015_ethz_mmm:exercise_2.3.zip you@eulerX ~$ unzip exercises:2015_ethz_mmm:exercise_2.3.zip
Go to the directory “exercise_2.3/”
you@eulerX ~$ cd exercise_2.3
- For the non-restrained optimizations to get A and B configurations, inp.a and inp.b
- For the restrained optimization along a chain, line_ij and inp_ff.templ, respectively the script to generate the “path” and the input file model for cp2k.
- For the line simulation with the dihedral parameters modified, (from 1x to 6x), ff_multiply_ij and ff_divide_ij.
- For the potential with varying parameters for the Psi dihedral angle, pot_psi.templ, that will be used by ff_multiply_ij and ff_divide_ij.
In this exercise, you are requested to start from the results of exercise 2, and perform the following steps
Choose two configurations A and B from the previously optimized grid (you can find them in the folder ~/exercise_2.2/Logs), close to the two minima. I suggest opt.1.4.pdb and opt.3.1.pdb.
you@eulerX exercise_2.3$ . ~/Scripts myfunctions.bash
To get help how to use the program simply type its name withot any argument, and press “Enter”
you@eulerX exercise_2.3$ m_pdbtorsion
The input file inp.a is similar to the one of exercise 2.2, but the “constraint” part was removed to perform a “free” geometry optimization. An important line is the initial configuration filename: ini.a.pdb Copy the opt.1.4.pdb into Minimum_a/ini.a.pdb.
Run cp2k with:
bsub cp2k.popt -i inp.a > out.a
Check the final psi and phi angles, in the file a_opt-pos-1.pdb. Note these angles on a piece of paper.
Go to the Minimum_b folder and do the same with inp.b (but now use opt.3.1.pdb as a starting point, not opt.1.4.pdb) , run cp2k in a similar way, and measure both torsion angles in the file b_opt-pos-1.pdb.
- Check the final energies (grep 'E =' b_opt-pos-1.pdb )
- copy the optimized a configuration into aopt.pdb.
- Substitute the values of the angles in the line_ij script, and generate a line (again using restraints to fix the dihedrals along this line). Again, this time you will have an output line with three columns (file eneline): the restrained phi, psi, and the energy in Hartree.
- <note important>1 Hartree=27.2116 eV=627.509 kcal/mol</note>
- In this way you will obtain an energy profile joining the two minima (would it be an idea to do a nudged elastic band?).
- Now, you can create a new directory, and use a different potential file where a dihedral angle is increased or decreased. This task is performed by the ff_multiply_ij script file, where you need again to substitute the values of the A and B pairs of angles to interpolate.
- This time different enemol* files will be generated, each for a modified strength of the bond parameters.
- Similarly, the ff_divide_ij will generate profiles with the strength divided by 2,3,4… in the files enediv.2, enediv.3, enediv.4…
- The mod_ff.gnu file will plot all that, and the shape of the harmonic dihedral potential.
- How will the line profile change? Why?